1. Field of the Invention
This invention relates to improving production levels of endogenous or heterologous polypeptides expressed in yeast by recombinant genetic means. In particular, the invention relates to the construction of high copy number recombinant expression constructs that produce elevated levels of stoichiometrically balanced amounts of trans-acting transcription factors that induce transcriptional activity in yeast. Specifically, the invention provides recombinant constructs encoding trans-acting transcription factors that regulate inducible expression of endogenous or heterologous polypeptides that are operatively linked to and expressed by regulatable promoters comprising cis-acting control elements responsive to said trans-acting transcription factors. The recombinant expression constructs of the invention express the encoded trans-acting transcription factors in amounts stoichiometrically-balanced to maintain the relative amounts thereof when expressed at elevated levels. The invention further provides methods for making modified yeast cells comprising the recombinant expression constructs of the invention. Also provided by the invention are yeast cells comprising said recombinant expression constructs of the invention. The invention provides methods for inducing high-level expression of endogenous or heterologous polypeptides in yeast cells containing the recombinant expression constructs of the invention. In certain embodiments, nucleic acid sequences encoding the endogenous or heterologous polypeptides and operatively linked to regulatable promoters comprising said cis-acting control elements are contained in recombinant expression constructs that also encode said trans-acting transcription factors. In alternative embodiments, nucleic acid sequences encoding the endogenous or heterologous polypeptides and operatively linked to regulatable promoters comprising said cis-acting control elements are contained in recombinant expression constructs separate and distinct from the recombinant expression constructs that encode said trans-acting transcription factors. In said alternative embodiments, the invention provides yeast cells comprising recombinant expression constructs encoding said trans-acting factors and also said recombinant expression constructs encoding said endogenous or heterologous polypeptides, whereby the abundance of each of the recombinant expression constructs in a substantial proportion of said cells is sufficiently high so as to provide high level production of the polypeptides encoded therein. The invention also provides polypeptides produced using the methods, constructs, and modified yeast cells of the invention.
2. Background of the Invention
Yeast, such as Saccharomyces cerevisiae, is an established host for expression of a variety of exogenously introduced, heterologous polypeptides using recombinant genetic technology. Expression levels of such recombinant polypeptides in yeast can reach levels greater than 10% of total cellular protein. Yeast is also a safe source of proteins for human and livestock consumption or for the production of therapeutic polypeptides. These properties make yeast a particularly useful host for genetic engineering and recombinant protein expression.
Expression of heterologous polypeptides in yeast has been accomplished in the prior art using recombinant expression constructs encoding the structural gene for the polypeptide to be expressed operatively linked to transcriptional control elements. Recombinant expression constructs containing these sequences also typically contained sequences allowing selection and amplification in both yeast and E. coli (Broach et al., 1979, Gene 8: 121-133; Rose and Broach, 1990, Methods Enzymol. 185: 234-279; Broach and Hicks, 1980, Cell 21: 501-508; Bolivar et al., 1977, Gene 2: 95-113). Of particular utility have been recombinant expression constructs containing the 2-micron circle plasmid of S. cerevisiae and the S. cerevisiae leu2- variant of the LEU2 gene allele. (Broach et al., 1979, Gene 8: 121-133; Rose and Broach, 1990, Methods Enzymol. 185: 234-279; Erhart and Hollenberg, 1983, J. Bacteriol. 156: 625-635). Such recombinant expression constructs have been reported to attain copy numbers of 100 to 500 or more per cell in yeast cells transformed therewith that were lacking the native 2-micron circle plasmid and were cultured in leucine-deficient growth media. High-level expression of polypeptides encoded in such recombinant expression constructs is possible because selection in leucine-deficient media in the presence of the inefficiently-selected leu2-d allele selects for yeast cells containing high copy numbers of the construct. An example of such a recombinant expression construct is the plasmid pC1/1 (See FIG. 2, Irani et al., 1987, Mol. Cell Biol. 7: 1233-1241).
Cis-acting elements and trans-acting factors of regulons such as the galactose regulon are useful for constructing recombinant expression constructs, wherein recombinant polypeptide expression can be induced and regulated in yeast cells transformed therewith. Particularly useful embodiments of such transformed yeast cells contain recombinant expression constructs in which expression is induced by culture conditions (e.g., by temperature, density, or the presence of a metabolite, nutrient, or other small molecule). Promoters activated by trans-acting factors from the galactose regulon are well known to be useful for inducing expression of recombinant polypeptides in yeast (Broach et al., 1979, Gene 8: 121-133). Promoters isolated in particular from the GAL1, GAL7 and GAL10 genes of the S. cerevisiae galactose regulon have been used extensively to achieve regulated expression of endogenous and heterologous polypeptides in yeast. These promoters are induced by addition of galactose to the culture media, and thus provide a cheap, non-toxic and convenient way to induce recombinant polypeptide expression.
The mechanisms that operate in galactose regulation of the GAL1, GAL7, and GAL10 promoters have been intensively studied (Johnston and Carlson, in The Molecular and Cellular Biology of the Yeast Saccharomyces: Gene Expression. Vol. 11: 193-281, 1992; Reece and Platt, 1997, Bioessays 19: 1001-1010). These promoters show little or no transcriptional activity and nearly undetectable levels of the GAL1, GAL7 and GAL10 gene transcripts or proteins in yeast cells cultured in the absence of galactose. However, within a few minutes after adding galactose to the yeast cell medium culture, the GAL1, GAL7 and GAL10 promoters are fully activated, resulting in greater than a 1000-fold increase in transcriptional activity (Johnston and Carlson, in The Molecular and Cellular Biology of the Yeast Saccharomyces: Gene Expression, Vol. 11: 193-281, 1992; Reece and Platt, 1997, Bioessays 19: 1001-1010).
This rapid and dramatic galactose induction of these promoters is known to be mediated by a protein complex consisting of three galactose regulon trans-acting factors: the proteins Gal3, Gal4 and Gal80 (see FIG. 1). The Gal4 protein binds to a specific seventeen base pair regulatory element (termed UASgal) upstream of the each of the GAL genes (Johnston and Carlson, in The Molecular and Cellular Biology of the Yeast Saccharomyces: Gene Expression, Vol. 11: 193-281, 1992; Reece and Platt, 1997, Bioessays 19: 1001-1010). In the absence of galactose in the culture media, the Gal4 protein binds to the UASgal binding site, but does not induce transcription (Koh et al., 1998, Molecular Cell 1: 895-904; Wu, et al., 1996, EMBO J. 15: 3951-3963); in this state, the Gal4 protein is tightly associated with another member of the complex, Gal80. In the presence of galactose, the Gal3 protein binds to Gal80, altering the Gal80-Gal4 protein interaction. This results in transcriptional activation of the GAL promoters by Gal4 (Johnston and Carlson, in The Molecular and Cellular Biology of the Yeast Saccharomyces: Gene Expression, Vol. 11:193-281, 1992; Reece and Platt, 1997, Bioessays 19: 1001-1010; Torchia and Hopper, 1986, Genetics 113: 229-246; Lue et al., Mol. Cell Biol. 7: 3446-3451, 1987; Suzuki-Fujimoto et al., 1996, Mol. Cell Biol. 16: 2504-2508).
Strong evidence indicates that proper regulation of transcription from galactose-inducible promoters requires a stoichiometric balance in the relative abundancies of the Gal3, Gal4 and Gal80 proteins (Johnston and Hopper, 1982, Proc. Natl. Acad. Sci. USA 79: 6971-6975; Hashimoto et al., 1983, Mol. Gen. Genet. 191: 31-38; Nogi et al., 1984, Mol Gen. Genet. 195: 29-34; Bhat and Hopper, 1992, Mol. Cell Biol. 12: 2701-2707). The natural abundance of each of these proteins in yeast cells is low, particularly that of Gal4 (Laughon and Gesteland, 1982, Proc. Nat'l. Acad. Sci. U.S.A. 79: 6827-6831). Gal4 has also been shown to be rate-limiting for expression of native, chromosomal, single-copy genes expressed via GAL promoters in the galactose regulon, i.e., the level of transcriptional activity of the structural genes of the galactose regulon depends on the amount of Gal4 produced in the cell (Johnston and Hopper, 1982, Proc. Natl. Acad. Sci. USA 79: 6971-6975). The extremely low level of Gal4 in native yeast cells has proved to be a serious impediment to the use of high-copy number, GAL promoter-containing recombinant expression constructs to produce high levels of recombinant polypeptides.
In addition, it turns out that Gal4 cannot simply be over-expressed to overcome these difficulties. In doing so, the normal stoichiometric balance between Gal4, Gal80 and Gal3 is upset, and Gal4 becomes a constitutive transcriptional element that stimulates expression in the absence of galactose in the culture media (Johnston and Hopper, 1982, Proc. Natl. Acad. Sci. USA 79: 6971-6975). An additional complication is that high levels of the Gal4 protein, unbalanced by corresponding stoichiometric levels of at least the Gal80 protein, are toxic to the cell (Laughon et al., 1984, Molec. Cell. Biol. 4: 268; Gill & Ptashne, 1988, Nature 334: 721-724; Mylin et al., 1990, in Methods in Enzymology, Colowick and Kaplan, eds., Vol. 185, pp. 297-308; Martegani et al., 1993, Yeast 9: 575-582; Mylin & Hopper, 1996, in Methods in Molecular Biology, Tuan, ed., Vol. 62). This loss of appropriate repression by Gal80 protein in constructs depending on Gal4 transcriptional activation seriously limits the usefulness of yeast cells transformed therewith, because it is advantageous to suppress transcriptional activity of the recombinant polypeptide until the cells reach high densities. This is often crucial in achieving high-level production of recombinant polypeptides, the expression of which often physiologically stresses the host cell and limits cell growth and division if recombinant polypeptides are produced at high levels prematurely. In fact, negative selective growth pressure against yeast cells producing such recombinant proteins results in a preponderance of cells in the culture that do not express high levels of the protein, thus rendering the culture an uneconomical source of recombinant polypeptide.
The prior art contains one attempt known to the present inventor at overcoming these intrinsic limitations of using galactose regulon trans-acting factors to provide regulated production of a recombinant polypeptide. This attempt consisted of expressing Gal4 using the GAL10 gene promoter (Mylin et al., 1990, Methods in Enzymology 185: 297-308). Unfortunately, the unusually high levels of Gal4 protein produced in these cells, unbalanced by Gal80 protein, were toxic: upon galactose induction, cell growth ceased and sustained production of recombinant polypeptide was not possible.
Thus, there is a need in the art for recombinant expression constructs and methods for inducing and regulating sustained high-level production of recombinant polypeptides in yeast.